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chasewnelson / SNPGenie

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
GNU General Public License v3.0
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sliding window error with new version compared to old version. #19

Closed mschoup closed 5 years ago

mschoup commented 5 years ago

Hi Chase

I'm very happy with SNPGenie and that you wrote in a way that has minimal requirements.
I have encountered an anomaly when using the current version compared to an old one I used previously.

The sliding window result file looks like this with the current version: file product first_site first_codon last_site last_codon sum_nonsyn_diffs sum_syn_diffs sum_nonsyn_sites sum_syn_sites piN piS piN/piS piN_vs_ref piS_vs_ref piN/piS_vs_ref WGS572_S13.vcf ORF 1 ATG 150 AGG 0 0 0 0 WGS572_S13.vcf ORF 4 AGC 153 AAG 0 0 0 0 WGS572_S13.vcf ORF 7 ACA 156 ACT 0 0 0 0 WGS572_S13.vcf ORF 10 AAT 159 TCC 0 0 0 0 WGS572_S13.vcf ORF 13 CCT 162 GAG 0 0 0 0

The sliding window result file looks like this with the old version: file product first_site first_codon last_site last_codon sum_nonsyn_diffs sum_syn_diffs sum_nonsyn_sites sum_syn_sites piN piS piN/piS piN_vs_ref piS_vs_ref piN/piS_vs_ref WGS572_S13.vcf ORF 1 ATG 150 AGG 0 0.0228922932049934 111.5 38.5 0 0.000594605018311517 0 0 0.000300779220779221 0 WGS572_S13.vcf ORF 4 AGC 153 AAG 0 0.0228922932049934 111.166666666667 38.8333333333333 0 0.000589501112574938 0 0 0.000298197424892704 0 WGS572_S13.vcf ORF 7 ACA 156 ACT 0 0.0228922932049934 110.5 39.5 0 0.000579551726708694 0 0 0.000293164556962025 0

I am running this command: snpgenie.pl --vcfformat=2 --snpreport=WGS572_S13.vcf --fastafile=WGS572_S13.consensus-map.fasta --minfreq=0.01 --slidingwindow=50 --gtffile=SNPGenie_orf.gff3

I have attached the files. SNPGenie-error.zip

Am I missing something obvious?

Best, Martin

singing-scientist commented 5 years ago

Thanks very much for using SNPGenie, Martin @mschoup, and apologies for the embarrassing bug. All values were reported as UNDEFINED (*) because I forgot to update expected new column names, which were implemented in an update, within the sliding window subroutine. That has now been fixed; please pull/download the new version and let me know if it works for you.

mschoup commented 5 years ago

I have just downloaded the new version and it is works. Thanks for the swift solution!

Martin